Yes. Epigenetic histone and direct DNA modifications occur due to enzymes that add or remove epigenetic tags. These enzymes, and the regulatory proteins that influence their activity, are of course encoded in the DNA. While phenotypic plasticity may occur to some extent without mutation, sustained and heritable changes (like the loss of the eye) do require mutations. Although the specific mutations leading to such loss are complicated and difficult to identify, the conclusion is not speculative.
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Iâm afraid you guys are running ahead of the real research. That happens. I understand. And frankly, it matters not even a little to me about the role of epigenetics and how it arises. I am just looking for a solid answer given current research. An honest answer as well. Thanks for your time.
Alright. And where is this research?
What real research have you looked up and read? There are at least 50 yearsâ worth of research papers on the topic.
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It is well established that you can change methylation patterns by changing the expression of both DNA methylases (the enzymes that methylate DNA) and demethylases. Epigenetics boils down to the same mechanisms as found in standard genes. There can be a whole host of possible mechanism, from mutations in the 3â UTR binding site for microRNA to mutations in a transcription factor binding site. There are many ways in which mutations can change gene expression.
You havenât yet read the paper you asked for earlier, which @Timothy_Horton provided to you. Iâm not going to assemble a comprehensive reading list for you on epigenetics, unless Iâm really convinced that you are serious about learning.
Your comments suggest that assembling the reading list really wouldnât be worth the effort.
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I have done real research on epigenetics, so I donât think that is the case. Iâm certainly not one of the worldâs top experts on epigenetics, but I have real world experience with it.
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Yes, I did. It is interesting but did not sound conclusive.
Great, then letâs discuss the specific points on which you disagree.
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So what would you say to someone who claimed inheritable traits, maybe even temporary, over a very short term in evolutionary timescales? Could these fish have become eyeless in a very short period of time? Is it even possible? If you answer âAbsolutely no wayâ, then are you going beyond the research? Are they as sure as you are about this?
Really? How did you manage to read and digest such a technically complex paper in one hour?
Where did you get your copy of the paper? It wasnât from above since my link shows it was only accessed 1 time which I did when I first posted to be sure the link worked. Oops!
ETA: I see the number just jumped to 2 meaning you finally got around to clicking on the link. 
You didnât read the paper at all, did you?
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Disagree? I did not disagree with anything in the paper. It sounded like good research to me, just not as conclusive as some here would state.
I would say exactly what I said in a previous post. Where is the evidence that these methylation patterns are present in gametes and single celled zygotes, and where is the evidence that these patterns are carried over through embryonic development? Thatâs the evidence we would need to see in order to conclude that these epigenetic traits are heritable.
Itâs possible that there is a biological system in these fish that can sense a lack of light which leads to changes in gene expression. This would fall under the category of phenotypic plasticity which also fits in just fine with standard evolutionary theory. It would be no different than someone getting a tan after being exposed to sunlight. The pathway from sensing light to DNA methylation would all be under the control of genes encoded by DNA, and mutations to those genes would affect the entire system.
If this were the case, then we would expect the phenotype to be reversible. From what I have read, it isnât. Therefore, it doesnât appear to be phenotypic plasticity. In the species with heritable epigenetic patterns we observe that the effects are reversible, so this again doesnât seem to be the mechanism in this case.
In all fairness, one of the two was me just a few minutes ago.
That sets r_speirâs count back to 0.
r_speir, where did you get your copy of the paper?
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Good. Sounds like there is still a lot of research to do. I know that other organisms seem to display epigenetic traits, so even after 50 years, it sounds like this still a very controversial subject. But apparently, your paradigm is satisfied that it is not in any way threatened by the findings.
What? I was able to open it some time ago. I read it an hour ago.
Not from the link I posted an hour ago. The counter shows you didnât access it there.
Where did you get your copy of the paper and how did you read it so quickly?
It isnât controversial at all. I would suspect that epigenetic traits are found in many animal clades. Epigenetics has been known to be important in mammalian development for quite a while.
Why would it be controversial?
It is just another layer of control over gene expression which is one of the most studied things in molecular biology. Epigenetics itself really isnât controversial.
You may be conflating epigenetics in general with transgenerational epigenetic inheritance (TEI) specifically. Claims made about TEI, especially in mammals, have been met with criticism and skepticism, but for good reason. There just isnât much evidence for it. Studies in humans show that almost all of the methylation patterns in cells are removed during the production of gametes, so there is no mechanism to transmit methylation patterns from one generation to another. However, DNA methylation is very important for controlling gene expression in human embryonic development, and this is absolutely non-controversial.
From you. This is what I opened